Sites

library(tidyverse)
library(cowplot)
library(maps)
library(ggforce)
library(viridis)

studies <- read_csv("../data/studies_gsheet.csv")
sites <- read_csv("../data/sites_gsheet.csv")

df <- studies %>% 
  group_by(site) %>% 
  summarise(Nstudies = n_distinct(studyID),
            Nspecies = n_distinct(species)) %>% 
  left_join(sites)

Joining, by = "site"

world <- map("world", plot = FALSE, fill = TRUE) %>% fortify()

# sanity check that coordinates are in the right country
# within a country, all Xs should be the same color
ggplot(df, aes(x = long, y = lat)) +
  geom_polygon(data = world, aes(group = group), col = "black", fill = "grey90") +
  geom_point(aes(col = country), size = 5, shape = 4, stroke = 2, alpha = .8) +
  coord_fixed(1.3, ylim = c(-55, 83.59961)) +
  scale_color_viridis_d() +
  theme_map() +
  guides(col = "none")

rr ggsave(../graphs/map.pdf, width = 20, height = 10, scale = 2)

Zoom in on sections

# japan
m1 <- m + 
  geom_polygon(data = world, aes(group = group), col = "black", fill = "grey90", lwd = .2) +
  geom_point(aes(size = Nstudies, fill = Nstudies), shape = 21, alpha = .8) +
  coord_fixed(1.3, ylim = c(25, 45), xlim = c(125, 145)) +
  theme(legend.position = "none") +
  panel_border(color = "grey", size = .5)
# europe
m2 <- m + 
  geom_polygon(data = world, aes(group = group), col = "black", fill = "grey90", lwd = .2) +
  geom_point(aes(size = Nstudies, fill = Nstudies), shape = 21, alpha = .8) +
  coord_fixed(1.3, ylim = c(32, 60), xlim = c(-10, 30)) +
  theme(legend.position = "none") +
  panel_border(color = "grey", size = .5)
# contiguous us
usa = map("state", plot = FALSE, fill = TRUE) %>% fortify() # "usa"
m3 <- m + 
  geom_polygon(data = world, aes(group = group), col = "black", fill = "grey90", lwd = .2) +
  geom_polygon(data = usa, aes(group = group), col = "black", fill = "grey90", lwd = .2) +
  geom_point(aes(size = Nstudies, fill = Nstudies), shape = 21, alpha = .8) +
  coord_fixed(1.3, ylim = c(25, 49), xlim = c(-127, -67)) +
  theme(legend.position = "none") +
  panel_border(color = "grey", size = .5)

leg <- plot_grid(NA, legend, ncol = 1, rel_heights = c(.1, .9), labels = c("", "Number of Studies"), label_x = -.35)

Cannot convert object of class logical into a grob.

bottom_row <- plot_grid(m3, m2, NA, m1, NA, leg, nrow = 1, rel_widths = c(2, 1.18, .06, .85, .08, .7))

Removed 3 rows containing missing values (geom_point).Removed 3 rows containing missing values (geom_point).Removed 3 rows containing missing values (geom_point).Removed 3 rows containing missing values (geom_point).Cannot convert object of class logical into a grob.Removed 3 rows containing missing values (geom_point).Removed 3 rows containing missing values (geom_point).Cannot convert object of class logical into a grob.

plot_grid(mx, bottom_row, ncol = 1, rel_heights = c(2.4, 1)) +
  theme(plot.margin = unit(c(.5, .5, 1.5, .5), "cm"))

Removed 3 rows containing missing values (geom_point).

ggsave("../graphs/map_insets.pdf", width = 8, height = 5.5, scale = 2)

Color = No species

ms <- ggplot(df, aes(x = long, y = lat)) +
  geom_polygon(data = world, aes(group = group), fill = "grey90") +
  geom_point(aes(size = Nstudies, fill = Nspecies), shape = 21, alpha = .8) +
  theme_map() +
  # # to make fill into discrete; overlap with size legend
  # scale_size_area("Number of\nStudies", max_size = 15) +
  # scale_fill_viridis_c("Number of\nStudies", guide = "legend") +
  # to have them side by side
  scale_fill_gradientn("", breaks = c(1, 11), colours = c("#598cde","#d4e324", "black")) +
  scale_size_area("", max_size = 15, breaks = c(1, 20, 40, 60)) +
  theme(legend.box = "horizontal") +
  guides(fill = guide_colorbar(reverse = T, barheight = 9.5, order = 1), 
         size = guide_legend(keyheight = 2.6, title.theme = element_text(size = 4)))
legend <- get_legend(ms)

Removed 3 rows containing missing values (geom_point).

# plot_grid(legend)
msx <- ms +
  annotate("rect", ymin = c(24, 31, 24), ymax = c(46, 62, 50), xmin = c(124, -12, -130), 
           xmax = c(146, 32, -64), size = .5, col = "grey", fill = NA) + 
  coord_fixed(1.3, ylim = c(-55, 83.59961)) +
  theme(legend.position = "none")

Zoom in on sections

# japan
ms1 <- ms + 
  geom_polygon(data = world, aes(group = group), col = "black", fill = "grey90", lwd = .2) +
  geom_point(aes(size = Nstudies, fill = Nspecies), shape = 21, alpha = .8) +
  coord_fixed(1.3, ylim = c(25, 45), xlim = c(125, 145)) +
  theme(legend.position = "none") +
  panel_border(color = "grey", size = .5)
# europe
ms2 <- ms + 
  geom_polygon(data = world, aes(group = group), col = "black", fill = "grey90", lwd = .2) +
  geom_point(aes(size = Nstudies, fill = Nspecies), shape = 21, alpha = .8) +
  coord_fixed(1.3, ylim = c(32, 60), xlim = c(-10, 30)) +
  theme(legend.position = "none") +
  panel_border(color = "grey", size = .5)
# contiguous us
usa = map("state", plot = FALSE, fill = TRUE) %>% fortify() # "usa"
ms3 <- ms + 
  geom_polygon(data = world, aes(group = group), col = "black", fill = "grey90", lwd = .2) +
  geom_polygon(data = usa, aes(group = group), col = "black", fill = "grey90", lwd = .2) +
  geom_point(aes(size = Nstudies, fill = Nspecies), shape = 21, alpha = .8) +
  coord_fixed(1.3, ylim = c(25, 49), xlim = c(-127, -67)) +
  theme(legend.position = "none") +
  panel_border(color = "grey", size = .5)

legs <- plot_grid(NA, legend, ncol = 2, rel_heights = c(.1, .9), labels = c("Species", "Studies"), label_x = -.1)

Cannot convert object of class logical into a grob.

bottom_row <- plot_grid(ms3, ms2, NA, ms1, NA, legs, nrow = 1, rel_widths = c(2, 1.18, .06, .85, .08, .7))

Removed 3 rows containing missing values (geom_point).Removed 3 rows containing missing values (geom_point).Removed 3 rows containing missing values (geom_point).Removed 3 rows containing missing values (geom_point).Cannot convert object of class logical into a grob.Removed 3 rows containing missing values (geom_point).Removed 3 rows containing missing values (geom_point).Cannot convert object of class logical into a grob.

plot_grid(msx, bottom_row, ncol = 1, rel_heights = c(2.4, 1)) +
  theme(plot.margin = unit(c(.5, .5, 1.5, .5), "cm"))

Removed 3 rows containing missing values (geom_point).

ggsave("../graphs/map_insets_col_species.pdf", width = 8, height = 5.5, scale = 2)

---

Session Info

rr sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] viridis_0.5.1     viridisLite_0.3.0 ggforce_0.3.1     maps_3.3.0        cowplot_1.0.0    
 [6] forcats_0.4.0     stringr_1.4.0     dplyr_0.8.3       purrr_0.3.2       readr_1.3.1      
[11] tidyr_1.0.0       tibble_2.1.3      ggplot2_3.2.1     tidyverse_1.2.1  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2         lubridate_1.7.4    lattice_0.20-38    prettyunits_1.0.2  ps_1.3.0          
 [6] assertthat_0.2.1   zeallot_0.1.0      digest_0.6.21      R6_2.4.0           cellranger_1.1.0  
[11] backports_1.1.5    stats4_3.6.1       evaluate_0.14      httr_1.4.1         pillar_1.4.2      
[16] rlang_0.4.0        lazyeval_0.2.2     readxl_1.3.1       rstudioapi_0.10    callr_3.3.2       
[21] rmarkdown_1.16     labeling_0.3       loo_2.1.0          polyclip_1.10-0    munsell_0.5.0     
[26] broom_0.5.2        compiler_3.6.1     modelr_0.1.5       xfun_0.10          rstan_2.19.2      
[31] base64enc_0.1-3    pkgconfig_2.0.3    pkgbuild_1.0.5     htmltools_0.4.0    tidyselect_0.2.5  
[36] gridExtra_2.3      matrixStats_0.55.0 crayon_1.3.4       withr_2.1.2        MASS_7.3-51.4     
[41] grid_3.6.1         nlme_3.1-141       jsonlite_1.6       gtable_0.3.0       lifecycle_0.1.0   
[46] magrittr_1.5       StanHeaders_2.19.0 scales_1.0.0       cli_1.1.0          stringi_1.4.3     
[51] farver_1.1.0       xml2_1.2.2         generics_0.0.2     vctrs_0.2.0        tools_3.6.1       
[56] glue_1.3.1         tweenr_1.0.1       hms_0.5.1          yaml_2.2.0         parallel_3.6.1    
[61] processx_3.4.1     inline_0.3.15      colorspace_1.4-1   rvest_0.3.4        knitr_1.25        
[66] haven_2.1.1